Bio Research

Skills (6)

Claude uses these on its own when your request matches.

• instrument-data-to-allotropeConvert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of…
• nextflow-developmentRun nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression,…
• scientific-problem-selectionThis skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific decisions. Use this skill when users ask to pitch a new research idea, work through a project problem, evaluate project…
• scvi-toolsDeep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with…
• single-cell-rna-qcPerforms quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering low-quality cells, assessing data quality, or following scverse/scanpy…
• startSet up your bio-research environment and explore available tools. Use when first getting oriented with the plugin, checking which literature, drug-discovery, or visualization MCP servers are connected, or surveying available analysis skills before starting a new project.

MCP servers (11)

Added to Claude Code when you install the plugin. You sign in to Bio Research the first time it is used.

• pubmedRemotehttps://pubmed.mcp.claude.com/mcp
• biorenderRemotehttps://mcp.services.biorender.com/mcp
• biorxivRemotehttps://hcls.mcp.claude.com/biorxiv/mcp
• consensusRemotehttps://mcp.consensus.app/mcp
• c-trialsRemotehttps://hcls.mcp.claude.com/clinical_trials/mcp
• chemblRemotehttps://hcls.mcp.claude.com/chembl/mcp
• synapseRemotehttps://mcp.synapse.org/mcp
• wileyRemotehttps://connector.scholargateway.ai/mcp
• owkinRemotehttps://mcp.k.owkin.com/mcp
• otRemotehttps://mcp.platform.opentargets.org/mcp
• benchlingRemote

Install

claude plugin marketplace add anthropics/knowledge-work-plugins && claude plugin install bio-research@knowledge-work-plugins

/plugin marketplace add anthropics/knowledge-work-plugins

/plugin install bio-research@knowledge-work-plugins